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- PDB-1l83: A CAVITY-CONTAINING MUTANT OF T4 LYSOZYME IS STABILIZED BY BURIED... -

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Basic information

Entry
Database: PDB / ID: 1l83
TitleA CAVITY-CONTAINING MUTANT OF T4 LYSOZYME IS STABILIZED BY BURIED BENZENE
ComponentsT4 LYSOZYME
KeywordsHYDROLASE(O-GLYCOSYL)
Function / homology
Function and homology information


viral release from host cell by cytolysis / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / host cell cytoplasm / defense response to bacterium
Similarity search - Function
Lysozyme - #40 / Endolysin T4 type / T4-type lysozyme / : / Glycoside hydrolase, family 24 / Phage lysozyme / Lysozyme domain superfamily / Lysozyme / Lysozyme-like domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / BENZENE / Endolysin
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / Resolution: 1.7 Å
AuthorsEriksson, A.E. / Matthews, B.W.
CitationJournal: Nature / Year: 1992
Title: A cavity-containing mutant of T4 lysozyme is stabilized by buried benzene.
Authors: Eriksson, A.E. / Baase, W.A. / Wozniak, J.A. / Matthews, B.W.
History
DepositionJan 21, 1992Processing site: BNL
Revision 1.0Oct 31, 1993Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 700SHEET THERE ARE SEVERAL SUBTLE ASPECTS OF THE SECONDARY STRUCTURE OF THIS MOLECULE WHICH CANNOT ...SHEET THERE ARE SEVERAL SUBTLE ASPECTS OF THE SECONDARY STRUCTURE OF THIS MOLECULE WHICH CANNOT CONVENIENTLY BE REPRESENTED IN HELIX AND SHEET RECORDS BELOW. THESE ASPECTS INFLUENCE THE REPRESENTATION OF HELIX 6 AND STRAND 3 OF SHEET *S1*. THE PAPER J.MOL.BIOL., V. 118, P. 81, 1978 SHOULD BE CONSULTED FOR THESE SUBTLETIES.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: T4 LYSOZYME
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,8926
Polymers18,5861
Non-polymers3055
Water2,558142
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.900, 60.900, 96.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Atom site foot note1: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. THIS ENTRY DOES NOT INCLUDE RESIDUES 163 AND 164.
2: SEO 901 FORMS AN S-S LINKAGE TO SEO 902.

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Components

#1: Protein T4 LYSOZYME


Mass: 18586.283 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Plasmid: M13 / References: UniProt: P00720, lysozyme
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS
#4: Chemical ChemComp-BNZ / BENZENE


Mass: 78.112 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H6
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 142 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal grow
*PLUS
pH: 6.7 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
12.3 Mphosphate1reservoir
20.23 M1reservoirNaCl
32-hydroxyethyl disulphide1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 1.7 Å / Num. obs: 14844 / % possible obs: 63 % / Rmerge(I) obs: 0.061

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Processing

SoftwareName: TNT / Classification: refinement
RefinementRfactor obs: 0.152 / Highest resolution: 1.7 Å
Details: RESIDUES 162 - 164 IN WILD-TYPE AND ALL MUTANT LYSOZYMES ARE EXTREMELY MOBILE. THUS THE COORDINATES FOR THESE RESIDUES ARE VERY UNRELIABLE. THIS ENTRY DOES NOT INCLUDE RESIDUES 163 AND 164.
Refinement stepCycle: LAST / Highest resolution: 1.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1289 0 2 156 1447
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.014
X-RAY DIFFRACTIONt_angle_deg1.9
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Refinement
*PLUS
Highest resolution: 1.7 Å / Rfactor obs: 0.152
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDType
X-RAY DIFFRACTIONt_angle_d
X-RAY DIFFRACTIONt_angle_deg

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